NCBI C++ ToolKit
Public Types | Public Member Functions | Static Public Member Functions | Private Types | Private Member Functions | Private Attributes | List of all members

Represents ASN.1 type BioSource defined in file seqfeat.asn

Search Toolkit Book for CBioSource_Base

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#include <objects/seqfeat/BioSource_.hpp>

+ Inheritance diagram for CBioSource_Base:
+ Collaboration diagram for CBioSource_Base:

Public Types

enum  EGenome {
  eGenome_unknown = 0 , eGenome_genomic = 1 , eGenome_chloroplast = 2 , eGenome_chromoplast = 3 ,
  eGenome_kinetoplast = 4 , eGenome_mitochondrion = 5 , eGenome_plastid = 6 , eGenome_macronuclear = 7 ,
  eGenome_extrachrom = 8 , eGenome_plasmid = 9 , eGenome_transposon = 10 , eGenome_insertion_seq = 11 ,
  eGenome_cyanelle = 12 , eGenome_proviral = 13 , eGenome_virion = 14 , eGenome_nucleomorph = 15 ,
  eGenome_apicoplast = 16 , eGenome_leucoplast = 17 , eGenome_proplastid = 18 , eGenome_endogenous_virus = 19 ,
  eGenome_hydrogenosome = 20 , eGenome_chromosome = 21 , eGenome_chromatophore = 22 , eGenome_plasmid_in_mitochondrion = 23 ,
  eGenome_plasmid_in_plastid = 24
}
 biological context More...
 
enum  EOrigin {
  eOrigin_unknown = 0 , eOrigin_natural = 1 , eOrigin_natmut = 2 , eOrigin_mut = 3 ,
  eOrigin_artificial = 4 , eOrigin_synthetic = 5 , eOrigin_other = 255
}
 
enum class  E_memberIndex {
  e__allMandatory = 0 , e_genome , e_origin , e_org ,
  e_subtype , e_is_focus , e_pcr_primers
}
 
typedef int TGenome
 
typedef int TOrigin
 
typedef COrg_ref TOrg
 
typedef list< CRef< CSubSource > > TSubtype
 
typedef CPCRReactionSet TPcr_primers
 
typedef Tparent::CMemberIndex< E_memberIndex, 7 > TmemberIndex
 
- Public Types inherited from CObject
enum  EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern }
 Control filling of newly allocated memory. More...
 
typedef CObjectCounterLocker TLockerType
 Default locker type for CRef. More...
 
typedef atomic< Uint8TCounter
 Counter type is CAtomiCounter. More...
 
typedef Uint8 TCount
 Alias for value type of counter. More...
 

Public Member Functions

 CBioSource_Base (void)
 
virtual ~CBioSource_Base (void)
 
 DECLARE_INTERNAL_TYPE_INFO ()
 
bool IsSetGenome (void) const
 Check if a value has been assigned to Genome data member. More...
 
bool CanGetGenome (void) const
 Check if it is safe to call GetGenome method. More...
 
void ResetGenome (void)
 Reset Genome data member. More...
 
void SetDefaultGenome (void)
 Assign default value to Genome data member. More...
 
TGenome GetGenome (void) const
 Get the Genome member data. More...
 
void SetGenome (TGenome value)
 Assign a value to Genome data member. More...
 
TGenomeSetGenome (void)
 Assign a value to Genome data member. More...
 
bool IsSetOrigin (void) const
 Check if a value has been assigned to Origin data member. More...
 
bool CanGetOrigin (void) const
 Check if it is safe to call GetOrigin method. More...
 
void ResetOrigin (void)
 Reset Origin data member. More...
 
void SetDefaultOrigin (void)
 Assign default value to Origin data member. More...
 
TOrigin GetOrigin (void) const
 Get the Origin member data. More...
 
void SetOrigin (TOrigin value)
 Assign a value to Origin data member. More...
 
TOriginSetOrigin (void)
 Assign a value to Origin data member. More...
 
bool IsSetOrg (void) const
 Check if a value has been assigned to Org data member. More...
 
bool CanGetOrg (void) const
 Check if it is safe to call GetOrg method. More...
 
void ResetOrg (void)
 Reset Org data member. More...
 
const TOrgGetOrg (void) const
 Get the Org member data. More...
 
void SetOrg (TOrg &value)
 Assign a value to Org data member. More...
 
TOrgSetOrg (void)
 Assign a value to Org data member. More...
 
bool IsSetSubtype (void) const
 Check if a value has been assigned to Subtype data member. More...
 
bool CanGetSubtype (void) const
 Check if it is safe to call GetSubtype method. More...
 
void ResetSubtype (void)
 Reset Subtype data member. More...
 
const TSubtypeGetSubtype (void) const
 Get the Subtype member data. More...
 
TSubtypeSetSubtype (void)
 Assign a value to Subtype data member. More...
 
bool IsSetIs_focus (void) const
 to distinguish biological focus Check if a value has been assigned to Is_focus data member. More...
 
bool CanGetIs_focus (void) const
 Check if value of Is_focus member is getatable. More...
 
void ResetIs_focus (void)
 Reset Is_focus data member. More...
 
void SetIs_focus (void)
 Set NULL data member (assign 'NULL' value to Is_focus data member). More...
 
bool IsSetPcr_primers (void) const
 Check if a value has been assigned to Pcr_primers data member. More...
 
bool CanGetPcr_primers (void) const
 Check if it is safe to call GetPcr_primers method. More...
 
void ResetPcr_primers (void)
 Reset Pcr_primers data member. More...
 
const TPcr_primersGetPcr_primers (void) const
 Get the Pcr_primers member data. More...
 
void SetPcr_primers (TPcr_primers &value)
 Assign a value to Pcr_primers data member. More...
 
TPcr_primersSetPcr_primers (void)
 Assign a value to Pcr_primers data member. More...
 
virtual void Reset (void)
 Reset the whole object. More...
 
- Public Member Functions inherited from CSerialObject
 CSerialObject (void)
 
virtual ~CSerialObject (void)
 
virtual const CTypeInfoGetThisTypeInfo (void) const =0
 
virtual void Assign (const CSerialObject &source, ESerialRecursionMode how=eRecursive)
 Set object to copy of another one. More...
 
virtual bool Equals (const CSerialObject &object, ESerialRecursionMode how=eRecursive) const
 Check if both objects contain the same values. More...
 
virtual void DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
void ThrowUnassigned (TMemberIndex index) const
 
void ThrowUnassigned (TMemberIndex index, const char *file_name, int file_line) const
 
bool HasNamespaceName (void) const
 Check if object data type has namespace name. More...
 
const stringGetNamespaceName (void) const
 Get namespace name. More...
 
bool HasNamespacePrefix (void) const
 Check if data type has namespace prefix. More...
 
const stringGetNamespacePrefix (void) const
 Get namespace prefix. More...
 
- Public Member Functions inherited from CObject
 CObject (void)
 Constructor. More...
 
 CObject (const CObject &src)
 Copy constructor. More...
 
virtual ~CObject (void)
 Destructor. More...
 
CObjectoperator= (const CObject &src) THROWS_NONE
 Assignment operator. More...
 
bool CanBeDeleted (void) const THROWS_NONE
 Check if object can be deleted. More...
 
bool IsAllocatedInPool (void) const THROWS_NONE
 Check if object is allocated in memory pool (not system heap) More...
 
bool Referenced (void) const THROWS_NONE
 Check if object is referenced. More...
 
bool ReferencedOnlyOnce (void) const THROWS_NONE
 Check if object is referenced only once. More...
 
void AddReference (void) const
 Add reference to object. More...
 
void RemoveReference (void) const
 Remove reference to object. More...
 
void ReleaseReference (void) const
 Remove reference without deleting object. More...
 
virtual void DoNotDeleteThisObject (void)
 Mark this object as not allocated in heap – do not delete this object. More...
 
virtual void DoDeleteThisObject (void)
 Mark this object as allocated in heap – object can be deleted. More...
 
void * operator new (size_t size)
 Define new operator for memory allocation. More...
 
void * operator new[] (size_t size)
 Define new[] operator for 'array' memory allocation. More...
 
void operator delete (void *ptr)
 Define delete operator for memory deallocation. More...
 
void operator delete[] (void *ptr)
 Define delete[] operator for memory deallocation. More...
 
void * operator new (size_t size, void *place)
 Define new operator. More...
 
void operator delete (void *ptr, void *place)
 Define delete operator. More...
 
void * operator new (size_t size, CObjectMemoryPool *place)
 Define new operator using memory pool. More...
 
void operator delete (void *ptr, CObjectMemoryPool *place)
 Define delete operator. More...
 
- Public Member Functions inherited from CDebugDumpable
 CDebugDumpable (void)
 
virtual ~CDebugDumpable (void)
 
void DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const
 
void DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const
 
void DumpToConsole (void) const
 

Static Public Member Functions

static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() EGenome (void)
 Access to EGenome's attributes (values, names) as defined in spec. More...
 
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() EOrigin (void)
 Access to EOrigin's attributes (values, names) as defined in spec. More...
 
- Static Public Member Functions inherited from CSerialObject
static void SetVerifyDataThread (ESerialVerifyData verify)
 
static void SetVerifyDataGlobal (ESerialVerifyData verify)
 
static string UnassignedString (void)
 
static CStringUTF8 UnassignedStringUTF8 (void)
 
static char UnassignedByte (void)
 
- Static Public Member Functions inherited from CObject
static NCBI_XNCBI_EXPORT void ThrowNullPointerException (void)
 Define method to throw null pointer exception. More...
 
static NCBI_XNCBI_EXPORT void ThrowNullPointerException (const type_info &type)
 
static EAllocFillMode GetAllocFillMode (void)
 
static void SetAllocFillMode (EAllocFillMode mode)
 
static void SetAllocFillMode (const string &value)
 Set mode from configuration parameter value. More...
 
- Static Public Member Functions inherited from CDebugDumpable
static void EnableDebugDump (bool on)
 

Private Types

typedef CSerialObject Tparent
 

Private Member Functions

 CBioSource_Base (const CBioSource_Base &)
 
CBioSource_Baseoperator= (const CBioSource_Base &)
 

Private Attributes

Uint4 m_set_State [1]
 
int m_Genome
 
int m_Origin
 
CRef< TOrgm_Org
 
list< CRef< CSubSource > > m_Subtype
 
CRef< TPcr_primersm_Pcr_primers
 

Additional Inherited Members

- Static Public Attributes inherited from CSerialObject
static const char * ms_UnassignedStr = "<*unassigned*>"
 
static const char ms_UnassignedByte = char(0xcd)
 
- Static Public Attributes inherited from CObject
static const TCount eCounterBitsCanBeDeleted = 1 << 0
 Define possible object states. More...
 
static const TCount eCounterBitsInPlainHeap = 1 << 1
 Heap signature was found. More...
 
static const TCount eCounterBitsPlaceMask
 Mask for 'in heap' state flags. More...
 
static const int eCounterStep = 1 << 2
 Skip over the "in heap" bits. More...
 
static const TCount eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
 Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...
 
static const TCount eCounterStateMask
 Valid object, and object in heap. More...
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Detailed Description

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BioSource gives the source of the biological material for sequences

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CBioSource_Base

Definition at line 84 of file BioSource_.hpp.


The documentation for this class was generated from the following files:
Modified on Fri Mar 29 09:51:36 2024 by modify_doxy.py rev. 669887